Re: [Phonopy-users] Runtime Error running phonopy-gruneisen

[Amir B. <ami...@gm...>]

Hi Dr. Togo,

I did as you suggested and the problem with getting errors doing the
wavevector analysis is somehow solved but now I get the following error
with both wavevector and frequency analyses.

/home/amir/.local/lib/python3.8/site-packages/phonopy/gruneisen/core.py:135:
RuntimeWarning: invalid value encountered in true_divide
  self._gruneisen = -edDe / self._delta_strain / self._eigenvalues / 2

I also tried--cutooff=0.001 and --cutoff=1 but still get the same error. I
would appreciate your suggestions solving this issue.

Best regards,
Amir

On Thu, Jan 20, 2022 at 3:51 PM Atsushi Togo <atz...@gm...> wrote:

> Hi,
>
> For your second problem, I guess you have to specify --qe option.
> For your first question, you may try adjusting the --cutoff option
> value to eliminate phonons whose frequencies are close to zero.
>
> Togo
>
> On Fri, Jan 21, 2022 at 6:02 AM Amir Behbahanian
> <ami...@gm...> wrote:
> >
> > Hi All,
> >
> > I ran tests on a copper in its primitive structure using quantum
> espresso. I was able to calculate all the possible properties using phonopy
> except the modal gruneisen parameters.
> >
> > I ran the reciprocal space command;
> >
> > phonopy-gruneisen --qe orig plus minus --dim="3 3 3" --pa="auto"
> --mesh="30 30 30" -p -c Cu-primitive.in
> >
> > and got the following error:
> >
> > Unit cell was read from "orig/Cu-primitive.in".
> > Force sets were read from "orig/FORCE_SETS".
> >
> > Unit cell was read from "plus/Cu-primitive.in".
> > Force sets were read from "plus/FORCE_SETS".
> >
> > Unit cell was read from "minus/Cu-primitive.in".
> > Force sets were read from "minus/FORCE_SETS".
> >
> >
> /home/amir/.local/lib/python3.8/site-packages/phonopy/gruneisen/core.py:135:
> RuntimeWarning: invalid value encountered in true_divide
> >   self._gruneisen = -edDe / self._delta_strain / self._eigenvalues / 2
> >
> > I also tried the command that is based on wavevectors;
> >
> > phonopy-gruneisen orig plus minus --dim="3 3 3" --pa="0 1/2 1/2 1/2 0
> 1/2 1/2 1/2 0" --band="0.0 0.0 0.0  0.0 0.5 0.5  0.25 0.75 0.5  0.0 0.5
> 0.5  0.0 0.0 0.0" -p -c Cu-primitive.in
> >
> > and got this set of errors:
> >
> > Unit cell was read from "orig/Cu-primitive.in".
> > Force sets were read from "orig/FORCE_SETS".
> > Traceback (most recent call last):
> >   File
> "/home/amir/.local/lib/python3.8/site-packages/phonopy/cui/load_helper.py",
> line 264, in _read_crystal_structure
> >     return read_crystal_structure(filename=filename,
> interface_mode=interface_mode)
> >   File
> "/home/amir/.local/lib/python3.8/site-packages/phonopy/interface/calculator.py",
> line 391, in read_crystal_structure
> >     unitcell = read_vasp(cell_filename)
> >   File
> "/home/amir/.local/lib/python3.8/site-packages/phonopy/interface/vasp.py",
> line 203, in read_vasp
> >     return _get_atoms_from_poscar(lines, symbols)
> >   File
> "/home/amir/.local/lib/python3.8/site-packages/phonopy/interface/vasp.py",
> line 216, in _get_atoms_from_poscar
> >     scale = float(lines[1])
> > ValueError: could not convert string to float: '  ibrav = 0\n'
> >
> > During handling of the above exception, another exception occurred:
> >
> > Traceback (most recent call last):
> >   File "/home/amir/.local/bin/phonopy-gruneisen", line 409, in <module>
> >     main(get_options())
> >   File "/home/amir/.local/bin/phonopy-gruneisen", line 304, in main
> >     phonon = phonopy.load(
> >   File
> "/home/amir/.local/lib/python3.8/site-packages/phonopy/cui/load.py", line
> 211, in load
> >     cell, smat, pmat = load_helper.get_cell_settings(
> >   File
> "/home/amir/.local/lib/python3.8/site-packages/phonopy/cui/load_helper.py",
> line 75, in get_cell_settings
> >     cell, optional_structure_info = _read_crystal_structure(
> >   File
> "/home/amir/.local/lib/python3.8/site-packages/phonopy/cui/load_helper.py",
> line 274, in _read_crystal_structure
> >     raise RuntimeError("\n".join(msg))
> > RuntimeError: ============================ phonopy.load
> ============================
> >   Reading crystal structure file failed in phonopy.load.
> >   Maybe phonopy.load(..., calculator='<calculator name>') expected?
> > ============================ phonopy.load ============================
> >
> > I would appreciate your comment on the problem. Please also find the
> related files attached.
> >
> > Regards,
> > Amir
> > _______________________________________________
> > Phonopy-users mailing list
> > Pho...@li...
> > https://lists.sourceforge.net/lists/listinfo/phonopy-users
>
>
>
> --
> Atsushi Togo
>
>
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